NEchols at lbl.gov
Wed May 20 10:00:40 PDT 2009
> I am new to phenix. I am tring to refine the occupancies
> using the phenix.refine gui. In the refinement settings- refinement
> strategy : occupancies , when I define the groups for individual
> atoms as chain A and resseq 1:200 (for protein atoms) and a ligand
> group in constrained as chain B and resseq 1:10 and chain C and
> resseq 1:10, the refinement fails with several errors. The
> refinement runs fine when I do not touch the "occupancies" panel on
> the gui.
Actually, right now the GUI doesn't handle all of the options for
occupancy groups - they were too complicated to generate the interface
automatically. I'll see if I can fix this.
What are the errors you get, and could you please describe your
structure in more detail? Based on the above, I don't think you want
to refine occupancies for chain A - you only need to do this for atoms
that have alternate conformations or that really aren't 100% present
(e.g. ions, also some larger ligands). Is the ligand group in two
conformations or do you really have two different chains?
> How do I refine in Phenix the occupancies defining as well as
> partitioning the molecule as individual, groups and coupled groups?
Right now you'll need to do this on the command line, but if you can
wait a day or two I may have this part of the GUI fixed. In version
1.4-3 and above, the parameters are this:
individual = None
remove_selection = None
selection = None
All of these may occur multiple times. The documentation says:
individual: Selection(s) for individual atoms. None is default which
is to refine the individual occupancies for atoms in alternative
conformations or for atoms with partial occupancies only.
remove_selection = Occupancies of selected atoms will not be refined
(even though they might satisfy the default criteria for occupancy
constrained_group = Selections to define constrained occupancies. If
only one selection is provided then one occupancy factor per selected
atoms will be refined and it will be constrained between predefined
max and min values.
Constrained groups are only required when you have two different sets
of atoms (e.g. different chains, or different residues in a single
chain, or a ligand/water and a protein chain, etc.) whose alternate
conformations are coupled.
Lawrence Berkeley Lab
NEchols at lbl.gov
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